recipe bioconductor-hicbricks

A flexible framework for storing and accessing high-resolution Hi-C data through HDF files. HiCBricks allows import of Hi-C data through various formats such as the 2D matrix format or a generalized n-column table formats. In terms of access, HiCBricks offers functions to retrieve values from genomic loci separated by a certain distance, or the ability to fetch matrix subsets using word alike terms. HiCBricks will at a later point offer the ability to fetch multiple matrix subsets using fewer calls. It offers the capacity to store GenomicRanges that may be associated to a particular Hi-C experiment, to do basic ranges overlap (any, within) with the Hi-C experiment associated Ranges object and also to store any metadata that users may think to be relevant for their Hi-C experiment. Finally, you can do TAD calls with LSD and create pretty heatmaps.

Homepage

https://bioconductor.org/packages/3.9/bioc/html/HiCBricks.html

License

MIT + file LICENSE

Recipe

/bioconductor-hicbricks/meta.yaml

package bioconductor-hicbricks

(downloads) docker_bioconductor-hicbricks

Versions

1.0.0-0

Depends bioconductor-biocfilecache

>=1.6.0,<1.7.0

Depends bioconductor-genomeinfodb

>=1.18.0,<1.19.0

Depends bioconductor-genomicranges

>=1.34.0,<1.35.0

Depends bioconductor-iranges

>=2.16.0,<2.17.0

Depends bioconductor-rhdf5

>=2.26.0,<2.27.0

Depends bioconductor-s4vectors

>=0.20.0,<0.21.0

Depends r-base

>=3.5.1,<3.5.2.0a0

Depends r-curl

Depends r-data.table

Depends r-digest

Depends r-ggplot2

Depends r-r6

Depends r-rappdirs

Depends r-rcolorbrewer

Depends r-reshape2

Depends r-scales

Depends r-stringr

Depends r-viridis

Requirements

Installation

With an activated Bioconda channel (see 2. Set up channels), install with:

conda install bioconductor-hicbricks

and update with:

conda update bioconductor-hicbricks

or use the docker container:

docker pull quay.io/biocontainers/bioconductor-hicbricks:<tag>

(see bioconductor-hicbricks/tags for valid values for <tag>)